{
  "_id": "6aa8f303089bafb098cf9ee4",
  "Package": "OSAT",
  "Type": "Package",
  "Title": "OSAT: Optimal Sample Assignment Tool",
  "Version": "1.61.0",
  "Author": "Li Yan",
  "Maintainer": "Li Yan <li.yan@roswellpark.org>",
  "Description": "A sizable genomics study such as microarray often involves\nthe use of multiple batches (groups) of experiment due to\npractical complication. To minimize batch effects, a careful\nexperiment design should ensure the even distribution of\nbiological groups and confounding factors across batches. OSAT\n(Optimal Sample Assignment Tool) is developed to facilitate the\nallocation of collected samples to different batches. With\nminimum steps, it produces setup that optimizes the even\ndistribution of samples in groups of biological interest into\ndifferent batches, reducing the confounding or correlation\nbetween batches and the biological variables of interest. It\ncan also optimize the even distribution of confounding factors\nacross batches. Our tool can handle challenging instances where\nincomplete and unbalanced sample collections are involved as\nwell as ideal balanced RCBD. OSAT provides a number of\npredefined layout for some of the most commonly used genomics\nplatform. Related paper can be find at\nhttp://www.biomedcentral.com/1471-2164/13/689 .",
  "URL": "http://www.biomedcentral.com/1471-2164/13/689",
  "License": "Artistic-2.0",
  "Collate": "AllClasses.R AllGenerics.R gAssembly-class.R gSample-class.R\ngSetup-class.R gUtils.R",
  "Packaged": {
    "Date": "2026-09-15 07:18:29 UTC",
    "User": "root"
  },
  "biocViews": "DataRepresentation, Visualization, ExperimentalDesign,\nQualityControl",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:36:39 UTC",
  "RemoteUrl": "https://github.com/bioc/OSAT",
  "RemoteRef": "HEAD",
  "RemoteSha": "2ca42305a28682c2650de81c46b70fa5c5813f93",
  "NeedsCompilation": "no",
  "_user": "bioc",
  "_type": "src",
  "_file": "OSAT_1.61.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/55c714bf932ff1bbbacb8f1320148ced08ed0602012a03ebf33ac901b8e52208",
  "_filesize": 1250533,
  "_sha256": "55c714bf932ff1bbbacb8f1320148ced08ed0602012a03ebf33ac901b8e52208",
  "_expires": "2026-12-24T07:25:53.000Z",
  "_created": "2026-09-15T07:18:29.000Z",
  "_published": "2026-09-15T07:25:55.349Z",
  "_bioccheck": {
    "error": 3,
    "warning": 6,
    "note": 14
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/34940768878",
  "_status": "success",
  "_upstream": "https://github.com/bioc/OSAT",
  "_commit": {
    "id": "2ca42305a28682c2650de81c46b70fa5c5813f93",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777379799
  },
  "_maintainer": {
    "name": "Li Yan",
    "email": "li.yan@roswellpark.org",
    "login": "yan16",
    "description": "",
    "uuid": 26777156
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 104289638180,
      "time": 136,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "10384814475"
    },
    {
      "job": 104289638248,
      "time": 147,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "10385805092"
    },
    {
      "job": 104289638241,
      "time": 131,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10385028422"
    },
    {
      "job": 104289638296,
      "time": 104,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "10385710867"
    },
    {
      "job": 104289638201,
      "time": 108,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10385546018"
    },
    {
      "job": 104288812992,
      "time": 187,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10385690197"
    },
    {
      "job": 104289638186,
      "time": 87,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10385565611"
    },
    {
      "job": 104289638316,
      "time": 76,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "10384878966"
    },
    {
      "job": 104289638385,
      "time": 70,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "10384779558"
    },
    {
      "job": 104289638236,
      "time": 63,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10384769553"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Depends"
    },
    {
      "package": "xtable",
      "role": "Suggests"
    },
    {
      "package": "Biobase",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.61.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.60.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "datarepresentation",
    "visualization",
    "experimentaldesign",
    "qualitycontrol"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 468,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 528,
    "source": "https://www.bioconductor.org/packages/stats/bioc/OSAT"
  },
  "_mentions": 12,
  "_searchresults": 10,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/OSAT.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "BeadChip96ToMSA4MAP",
    "create.experiment.setup",
    "create.optimized.setup",
    "exclude<-",
    "GenotypingChip",
    "get.experiment.setup",
    "getLayout",
    "IlluminaBeadChip",
    "IlluminaBeadChip24Plate",
    "IlluminaBeadChip48Plate",
    "IlluminaBeadChip96Plate",
    "initialize",
    "map.to.MSA",
    "metadata",
    "metadata<-",
    "MSA4.plate",
    "multi.barplot",
    "multi.chisq.test",
    "optimal.block",
    "optimal.shuffle",
    "plot",
    "predefined",
    "QC",
    "setup.container",
    "setup.sample",
    "show",
    "summary"
  ],
  "_datasets": [
    {
      "name": "BeadChip96ToMSA4MAP",
      "title": "Class '\"MSAroboticPlate\"'",
      "object": "predefined",
      "file": "predefined.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "MSA_plate",
        "MSA_ID",
        "chipRows",
        "chipColumns",
        "chips",
        "rows",
        "columns",
        "wells"
      ],
      "rows": 96,
      "table": true,
      "tojson": true
    },
    {
      "name": "gc",
      "title": "R data object based on example file.",
      "object": "example.setup",
      "file": "example.setup.RData",
      "class": [
        "gContainer"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "GenotypingChip",
      "title": "Class '\"BeadChip\"'",
      "object": "predefined",
      "file": "predefined.RData",
      "class": [
        "BeadChip"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "gs",
      "title": "R data object based on example file.",
      "object": "example.setup",
      "file": "example.setup.RData",
      "class": [
        "gSample"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "gSetup",
      "title": "R data object based on example file.",
      "object": "example.setup",
      "file": "example.setup.RData",
      "class": [
        "gExperimentSetup"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "gSetup2",
      "title": "R data object based on example file.",
      "object": "example.setup",
      "file": "example.setup.RData",
      "class": [
        "gExperimentSetup"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "IlluminaBeadChip",
      "title": "Class '\"BeadChip\"'",
      "object": "predefined",
      "file": "predefined.RData",
      "class": [
        "BeadChip"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "IlluminaBeadChip24Plate",
      "title": "Class '\"BeadPlate\"'",
      "object": "predefined",
      "file": "predefined.RData",
      "class": [
        "BeadPlate"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "IlluminaBeadChip48Plate",
      "title": "Class '\"BeadPlate\"'",
      "object": "predefined",
      "file": "predefined.RData",
      "class": [
        "BeadPlate"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "IlluminaBeadChip96Plate",
      "title": "Class '\"BeadPlate\"'",
      "object": "predefined",
      "file": "predefined.RData",
      "class": [
        "BeadPlate"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "MSA4.plate",
      "title": "Class '\"MSAroboticPlate\"'",
      "object": "predefined",
      "file": "predefined.RData",
      "class": [
        "MSAroboticPlate"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "pheno",
      "title": "R data object based on example file.",
      "object": "example.setup",
      "file": "example.setup.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "SampleType",
        "Race",
        "AgeGrp"
      ],
      "rows": 576,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "BeadChip-class",
      "title": "Class '\"BeadChip\"'",
      "topics": [
        "BeadChip-class",
        "GenotypingChip",
        "getLayout,BeadChip-method",
        "IlluminaBeadChip"
      ]
    },
    {
      "page": "BeadPlate-class",
      "title": "Class '\"BeadPlate\"'",
      "topics": [
        "BeadPlate-class",
        "IlluminaBeadChip24Plate",
        "IlluminaBeadChip48Plate",
        "IlluminaBeadChip96Plate"
      ]
    },
    {
      "page": "create.optimized.setup",
      "title": "Create optimized setup",
      "topics": [
        "create.optimized.setup"
      ]
    },
    {
      "page": "example.setup",
      "title": "R data object based on example file.",
      "topics": [
        "gc",
        "gs",
        "gSetup",
        "gSetup2",
        "pheno"
      ]
    },
    {
      "page": "gArray-class",
      "title": "Class '\"gArray\"'",
      "topics": [
        "dim,gArray-method",
        "gArray-class",
        "getLayout",
        "getLayout,gArray-method",
        "metadata",
        "metadata,gArray-method",
        "metadata<-",
        "metadata<-,gArray-method",
        "ncol,gArray-method",
        "nrow,gArray-method"
      ]
    },
    {
      "page": "gAssembly-class",
      "title": "Class '\"gAssembly\"'",
      "topics": [
        "gAssembly-class",
        "getLayout,gAssembly-method",
        "initialize,gAssembly-method",
        "metadata,gAssembly-method",
        "metadata<-,gAssembly-method",
        "show,gAssembly-method"
      ]
    },
    {
      "page": "gContainer-class",
      "title": "Class '\"gContainer\"'",
      "topics": [
        "cid,gContainer-method",
        "exclude<-",
        "exclude<-,gContainer-method",
        "gContainer-class",
        "get.gAssembly,gContainer-method",
        "getLayout,gContainer-method",
        "initialize,gContainer-method",
        "metadata,gContainer-method",
        "metadata<-,gContainer-method",
        "setup.container",
        "show,gContainer-method"
      ]
    },
    {
      "page": "get.experiment.setup",
      "title": "Get experiment assignment after optimization.",
      "topics": [
        "get.experiment.setup"
      ]
    },
    {
      "page": "gExperimentSetup-class",
      "title": "Class '\"gExperimentSetup\"'",
      "topics": [
        "create.experiment.setup",
        "get.gAssembly,gExperimentSetup-method",
        "gExperimentSetup-class",
        "initialize,gExperimentSetup-method",
        "metadata,gExperimentSetup-method",
        "metadata<-,gExperimentSetup-method",
        "samples,gExperimentSetup-method",
        "show,gExperimentSetup-method",
        "summary,gExperimentSetup-method"
      ]
    },
    {
      "page": "gPlate-class",
      "title": "Class '\"gPlate\"'",
      "topics": [
        "getLayout, gPlate-method",
        "gPlate-class",
        "initialize,gPlate-method",
        "show,gPlate-method"
      ]
    },
    {
      "page": "gSample-class",
      "title": "Class 'gSample'",
      "topics": [
        "gSample-class",
        "initialize,gSample-method",
        "setup.sample",
        "show,gSample-method",
        "summary",
        "summary,gSample-method"
      ]
    },
    {
      "page": "gSlide-class",
      "title": "Class '\"gSlide\"'",
      "topics": [
        "getLayout,gSlide-method",
        "gSlide-class",
        "initialize,gSlide-method",
        "show,gSlide-method"
      ]
    },
    {
      "page": "MSAroboticPlate-class",
      "title": "Class '\"MSAroboticPlate\"'",
      "topics": [
        "BeadChip96ToMSA4MAP",
        "getLayout,MSAroboticPlate-method",
        "initialize,MSAroboticPlate-method",
        "map.to.MSA",
        "map.to.MSA,data.frame,MSAroboticPlate-method",
        "map.to.MSA,gExperimentSetup,MSAroboticPlate-method",
        "MSA4.plate",
        "MSAroboticPlate-class",
        "show,MSAroboticPlate-method"
      ]
    },
    {
      "page": "multi.barplot",
      "title": "multi.barplot",
      "topics": [
        "multi.barplot"
      ]
    },
    {
      "page": "multi.chisq.test",
      "title": "multi.chisq.test",
      "topics": [
        "multi.chisq.test"
      ]
    },
    {
      "page": "optimal.block",
      "title": "optimal.block",
      "topics": [
        "optimal.block"
      ]
    },
    {
      "page": "optimal.shuffle",
      "title": "optimal.shuffle",
      "topics": [
        "optimal.shuffle"
      ]
    },
    {
      "page": "plot-methods",
      "title": "Methods for Function 'plot'",
      "topics": [
        "plot,gExperimentSetup,missing-method",
        "plot-methods"
      ]
    },
    {
      "page": "predefined",
      "title": "Show predefined objects in the package.",
      "topics": [
        "predefined"
      ]
    },
    {
      "page": "QC",
      "title": "QC",
      "topics": [
        "QC"
      ]
    }
  ],
  "_rundeps": [],
  "_vignettes": [
    {
      "source": "OSAT.Rnw",
      "filename": "OSAT.pdf",
      "title": "An introduction to OSAT",
      "engine": "utils::Sweave",
      "headings": [
        "Overview",
        "Demonstration",
        "Methodology review",
        "Classes and Methods",
        "Additional Case studies",
        "Discussion",
        "Session information"
      ],
      "created": "2013-11-01 20:26:13",
      "modified": "2013-11-01 20:26:13",
      "commits": 1
    }
  ],
  "_score": 4.301029995663981,
  "_indexed": true,
  "_nocasepkg": "osat",
  "_universes": [
    "bioc",
    "yan16"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.61.0",
      "date": "2026-09-15T07:20:55.000Z",
      "distro": "resolute",
      "commit": "2ca42305a28682c2650de81c46b70fa5c5813f93",
      "fileid": "https://r2.ropensci.org/0b28fc999df259bf47e10e6f2f4131ad5aa8213649f17b2e37b97dd2e57a44d6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/34940768878"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.61.0",
      "date": "2026-09-15T07:20:42.000Z",
      "distro": "resolute",
      "commit": "2ca42305a28682c2650de81c46b70fa5c5813f93",
      "fileid": "https://r2.ropensci.org/153a6f74cbd896d3afb20e952663bb60a9f80695e810b4c932e5a8ddd44fdce3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/34940768878"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.61.0",
      "date": "2026-09-15T07:25:19.000Z",
      "commit": "2ca42305a28682c2650de81c46b70fa5c5813f93",
      "fileid": "https://r2.ropensci.org/3024ab4ac4551bc2e5223eeb4f2afe044627c3fdecfd47d134d265362c15c525",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/34940768878"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.61.0",
      "date": "2026-09-15T07:21:39.000Z",
      "commit": "2ca42305a28682c2650de81c46b70fa5c5813f93",
      "fileid": "https://r2.ropensci.org/1cdf764c59b9cf8543d4cb057edb915d41f0fc01f950039732f0fc1135fb65f9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/34940768878"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.61.0",
      "date": "2026-09-15T07:20:14.000Z",
      "commit": "2ca42305a28682c2650de81c46b70fa5c5813f93",
      "fileid": "https://r2.ropensci.org/8913d82a69b071096b97cd772694f8c7cbdaa57838512598250eee25b0f3f604",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/34940768878"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.61.0",
      "date": "2026-09-15T07:19:38.000Z",
      "commit": "2ca42305a28682c2650de81c46b70fa5c5813f93",
      "fileid": "https://r2.ropensci.org/4cfe6a2bc6b0bc72ef22c1459f2956f3b75015e1811b6942c75687bbd75453bf",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/34940768878"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.61.0",
      "date": "2026-09-15T07:19:30.000Z",
      "commit": "2ca42305a28682c2650de81c46b70fa5c5813f93",
      "fileid": "https://r2.ropensci.org/9d2b7d6ca41f6e68d8834935142d4e14466fec341eccc1d0041a4aee77a8e0c1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/34940768878"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.61.0",
      "date": "2026-09-15T07:19:28.000Z",
      "commit": "2ca42305a28682c2650de81c46b70fa5c5813f93",
      "fileid": "https://r2.ropensci.org/b72c1571c51966bafe5798181224e68a375d6772c3fa961eade7dea857ad02e0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/34940768878"
    }
  ]
}